MathML, SMILES, FieldML, SBML, and CellML formats

[obi-bot]

MathML proposed def: MathML 2.0, a W3C Recommendation was released on 21 Feb 2001. A product of the W3C Math working group, MathML is a low-level specification for describing mathematics as a basis for machine to machine communication. It provides a much needed foundation for the inclusion of mathematical expressions in Web pages def src: http://www.w3.org/Math/

FieldML proposed def: FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible. def src: http://www.physiomeproject.org/xml\_languages/fieldml

SMILES proposed def: SMILES™ (Simplified Molecular Input Line Entry System) as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. SMILES™ contains the same information as is found in an extended connection table but with several advantages. A SMILES™ string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILES™ string symbolizing either a molecule or reaction. SMILES™ development was initiated by David Weininger in the late 1980s using the concept of a graph with nodes as atoms and edges as bonds to represent a molecule. Parentheses are used to indicate branching points and numeric labels designate ring connection points. The basic SMILES™ grammar also includes as well as isotopic information, configuration about double bonds, and chirality leading to what is known as isomeric SMILES™. Since its inception, SMILES™ has been modified and expanded by Daylight to include not only new features but two additional chemical languages: SMARTS®, an expansion of SMILES™ allowing specification of molecular patterns and properties for substructure searching with varying levels of specificity, and SMIRKS®, a restricted version of reaction SMARTS® involving changes in atom-bond patterns that define generic reactions. def src: http://www.daylight.com/smiles/

SBML proposed def: The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks in software. It's applicable to models of metabolism, cell-signaling, and many others. def src: http://sbml.org/

CellML proposed def: The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models, it has a broader application (for an example, see the classical Mooney-Rivlin Constitutive Material Law). CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). CellML includes mathematics and metadata by leveraging existing languages, including MathML and RDF. In the future, CellML may also use other existing languages to specify data and define simulation and rendering information. def src: http://www.cellml.org/

Reported by: bbug

Original Ticket: "obi/obi-terms/50":https://sourceforge.net/p/obi/obi-terms/50

[obi-bot]

• status: open --> closed

Original comment by: mcourtot

[obi-bot]

tracker closed after merging with https://sourceforge.net/tracker/index.php?func=detail&aid=2224768&group\_id=177891&atid=886178

Original comment by: mcourtot